Variant chr6-36371364-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_016135.4(ETV7):c.630G>A(p.Ala210Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,598,322 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0023 ( 15 hom. )

Consequence

ETV7
NM_016135.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.25

Variant links:

Genes affected

ETV7 (HGNC:18160): (ETS variant transcription factor 7) The protein encoded by this gene belongs to the ETS family of transcription factors, which is a large group of evolutionarily conserved transcriptional regulators that play an important role in a variety of cellular processes throughout development and differentiation, and are involved in oncogenesis as well. This protein is predominantly expressed in hematopoietic tissues. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene (PMID:11108721).[provided by RefSeq, May 2011]

ETV7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 6-36371364-C-T is Benign according to our data. Variant chr6-36371364-C-T is described in ClinVar as [Benign]. Clinvar id is 721447.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.25 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ETV7	NM_016135.4 linkuse as main transcript	c.630G>A	p.Ala210Ala	synonymous_variant	5/8	ENST00000340181.9	NP_057219.1	Q9Y603-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ETV7	ENST00000340181.9 linkuse as main transcript	c.630G>A	p.Ala210Ala	synonymous_variant	5/8	1	NM_016135.4	ENSP00000341843.4		Q9Y603-1

Frequencies

GnomAD3 genomes

AF:

0.00160

AC:

243

AN:

152242

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00262

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00496

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00184

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00216

AC:

482

AN:

223574

Hom.:

AF XY:

0.00242

AC XY:

293

AN XY:

120866

show subpopulations

Gnomad AFR exome

AF:

0.000146

Gnomad AMR exome

AF:

0.00147

Gnomad ASJ exome

AF:

0.00550

Gnomad EAS exome

AF:

0.000119

Gnomad SAS exome

AF:

0.00585

Gnomad FIN exome

AF:

0.000161

Gnomad NFE exome

AF:

0.00201

Gnomad OTH exome

AF:

0.00249

GnomAD4 exome

AF:

0.00230

AC:

3322

AN:

1445962

Hom.:

Cov.:

AF XY:

0.00244

AC XY:

1749

AN XY:

717854

show subpopulations

Gnomad4 AFR exome

AF:

0.000361

Gnomad4 AMR exome

AF:

0.00129

Gnomad4 ASJ exome

AF:

0.00602

Gnomad4 EAS exome

AF:

0.0000513

Gnomad4 SAS exome

AF:

0.00613

Gnomad4 FIN exome

AF:

0.000135

Gnomad4 NFE exome

AF:

0.00212

Gnomad4 OTH exome

AF:

0.00268

GnomAD4 genome

AF:

0.00160

AC:

244

AN:

152360

Hom.:

Cov.:

AF XY:

0.00172

AC XY:

128

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00261

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00517

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00184

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00152

Hom.:

Bravo

AF:

0.00155

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.96

DANN

Benign

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over